ggpLayerSpatAnnOutline: Add outline of spatial annotations

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add outline of spatial annotations

Description

Adds a ggplot2 layer of polygons visualizing the outline of spatial annotations.

Usage

ggpLayerSpatAnnOutline(
  object,
  ids = NULL,
  tags = NULL,
  test = "any",
  alpha = 0.5,
  fill = NA,
  line_alpha = 0.9,
  line_color = "black",
  line_size = 1,
  line_type = "solid",
  use_colors = FALSE,
  clrp = NULL,
  clrp_adjust = NULL,
  inner = TRUE,
  incl_edge = FALSE,
  merge_edge = FALSE,
  incr_vert = FALSE,
  expand_outline = NULL,
  xrange = getCoordsRange(object)$x,
  yrange = getCoordsRange(object)$y,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
tags	Character vector or NULL. If character, the tags for the image annotation selection. See section Selection of spatial annotations for more information.
test	Character value. One of c('any'. 'all', 'identical', 'not_identical', 'none'). Specifies how input for tags is used to select spatial annotations. See section Selection of spatial annotations for more information.
fill	Character value or NA. If character, specifies the color with which the outline of the spatial annotation is filled.
line_alpha	Numeric. Affects alpha of main lines of the plot.
line_color	Character. Affects color of the main lines of the plot.
line_size	Numeric. Affects size of the main lines of the plot.
line_type	Character. The line type. One of 'blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash' and 'twodash'.
use_colors	Logical value. If TRUE, the color aesthetic is used to display each outline in a different color while providing a legend.
clrp	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.
clrp_adjust	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.
inner	Logical value. If FALSE, only outer borders of the annotation are displayed.
incl_edge	Logical value. If TRUE, the function includes the tissue edge (see identifyTissueOutline()) in the visualization and removes the parts of the outline that transgress the tissues edge.
merge_edge	Logical value. If incl_edge = TRUE the outline of the tissue edge is used to replace the part of the annotation outline that was removed due to crossing the tissue edge.
incr_vert	Logical value. If TRUE, the number of vertices of the polygon to be plotted is increased by linear interpolation. This can lead to smoother visualization but also to increased runtime.
expand_outline	Distance measure by which the outline of the area is expanded.
xrange, yrange	Distance vector of length two or NULL. If not NULL, specifies the x- and y-range to which the spatial output is cropped. E.g. xrange = c(200, 500) results in the two dimensional space being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original range is used.
...	Used to absorb deprecated arguments or functions.

Value

ggpLayer*()-functions return lists of ggproto objects that can be added to ggplots via the + operator. In most of the cases they are supposed to be added to plots created with the plotSurface*() family.

Note

Adds two additional layers to set the scales for the color- and fill aesthetic of the plot.

expand_outline only works if inner is FALSE (or the spatial annotation does not contain any inner borders).

See Also

ggpLayerSpatAnnPointer()

Examples

library(SPATA2)
library(patchwork)

object <- loadExampleObject("UKF275T")

object <-
 createNumericAnnotations(
   object = object,
   variable = "HM_HYPOXIA",
   threshold = "kmeans_high",
   id = "hypoxia_ann",
   inner_borders = FALSE,
   force1 = TRUE
   )

# range of hypoxia annotation
hr <- getSpatAnnRange(object, id = "hypoxia_ann")

hr_ggpL <- ggpLayerSpatAnnOutline(object, ids = "hypoxia_ann")

plotSurface(object, "HM_HYPOXIA") + hr_ggpL

p_rect <-
 plotImage(object) +
 hr_ggpL +
 ggpLayerRect(object, xrange = hr$x, yrange = hr$y)

p_zoomed <-
 plotImage(object) +
 ggpLayerZoom(object, xrange = hr$x, yrange = hr$y)

p_rect + p_zoomed

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.